A special operations raid meant to disrupt a Taliban arms operation in southern Afghanistan ended in the death of a man with family ties to the Afghan presidentâ€™s inner circle, leading to tensions between regional officials and the military, officials say.

The conflict comes at a time of growing tensions over American Special Operations forces in the country, after President Hamid Karzai recently banned their operation in a critical province near the capital. And it highlighted a complex web of Afghan family and factional relations that has led provincial officials allied with Mr. Karzai to defend men that international military officials have identified as insurgents.